Receptor
PDB id Resolution Class Description Source Keywords
6N96 1.7 Å EC: 4.1.1.- METHYLMALONYL-COA DECARBOXYLASE IN COMPLEX WITH 2-SULFONATE- OXA(DETHIA)-COA ESCHERICHIA COLI (STRAIN K12) CROTONASE BETA-KETO ISOSTERE LYASE
Ref.: SULFONATE/NITRO BEARING METHYLMALONYL-THIOESTER ISO APPLIED TO METHYLMALONYL-COA DECARBOXYLASE STRUCTURE-FUNCTION STUDIES. J. AM. CHEM. SOC. V. 141 5121 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO5 F:302;
E:302;
D:302;
C:302;
B:302;
A:302;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Ki = 3.8 uM
887.595 C24 H40 N7 O21 P3 S C[C@H...
LCV C:301;
A:301;
C:303;
D:301;
F:301;
E:301;
F:303;
B:301;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
Atoms found LESS than expected: % Diff = 0;
none;
none;
none;
Atoms found LESS than expected: % Diff = 0;
none;
Ki = 3.8 uM
887.595 C24 H40 N7 O21 P3 S C[C@@...
IMD D:303;
Invalid;
none;
submit data
69.085 C3 H5 N2 c1c[n...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6N96 1.7 Å EC: 4.1.1.- METHYLMALONYL-COA DECARBOXYLASE IN COMPLEX WITH 2-SULFONATE- OXA(DETHIA)-COA ESCHERICHIA COLI (STRAIN K12) CROTONASE BETA-KETO ISOSTERE LYASE
Ref.: SULFONATE/NITRO BEARING METHYLMALONYL-THIOESTER ISO APPLIED TO METHYLMALONYL-COA DECARBOXYLASE STRUCTURE-FUNCTION STUDIES. J. AM. CHEM. SOC. V. 141 5121 2019
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 6N93 Ki = 20.6 uM KGA C24 H38 N8 O20 P3 CC(=[N+]([....
2 6N95 Ki = 7.5 uM YXR C24 H40 N7 O20 P3 S2 C[C@H](C(=....
3 6N96 Ki = 3.8 uM SO5 C24 H40 N7 O21 P3 S C[C@H](C(=....
4 6N92 Ki = 10.8 uM KFV C24 H38 N8 O19 P3 S CC(=[N+]([....
5 6N97 Ki = 7.1 uM KGP C24 H41 N8 O20 P3 S C[C@H](C(=....
6 6N94 Ki = 19.8 uM KGJ C24 H39 N9 O19 P3 CC(=[N+]([....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 6N93 Ki = 20.6 uM KGA C24 H38 N8 O20 P3 CC(=[N+]([....
2 6N95 Ki = 7.5 uM YXR C24 H40 N7 O20 P3 S2 C[C@H](C(=....
3 6N96 Ki = 3.8 uM SO5 C24 H40 N7 O21 P3 S C[C@H](C(=....
4 6N92 Ki = 10.8 uM KFV C24 H38 N8 O19 P3 S CC(=[N+]([....
5 6N97 Ki = 7.1 uM KGP C24 H41 N8 O20 P3 S C[C@H](C(=....
6 6N94 Ki = 19.8 uM KGJ C24 H39 N9 O19 P3 CC(=[N+]([....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1DUB Ki = 1.6 uM CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
2 1EY3 - DAK C32 H47 N8 O17 P3 S CC(C)(CO[P....
3 1MJ3 - HXC C27 H46 N7 O17 P3 S CCCCCC(=O)....
4 2DUB - CO8 C29 H50 N7 O17 P3 S CCCCCCCC(=....
5 6N95 Ki = 7.5 uM YXR C24 H40 N7 O20 P3 S2 C[C@H](C(=....
6 6N96 Ki = 3.8 uM SO5 C24 H40 N7 O21 P3 S C[C@H](C(=....
7 6N92 Ki = 10.8 uM KFV C24 H38 N8 O19 P3 S CC(=[N+]([....
8 6N97 Ki = 7.1 uM KGP C24 H41 N8 O20 P3 S C[C@H](C(=....
9 6N94 Ki = 19.8 uM KGJ C24 H39 N9 O19 P3 CC(=[N+]([....
10 5ZAI - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
11 5DTW Kd = 3.5 uM 5F9 C41 H74 N7 O17 P3 S CCCCCCCCCC....
12 5JBX - MLI C3 H2 O4 C(C(=O)[O-....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SO5; Similar ligands found: 164
No: Ligand ECFP6 Tc MDL keys Tc
1 SO5 1 1
2 LCV 1 1
3 KGP 0.84375 0.989691
4 YZS 0.84375 0.989691
5 YXR 0.825758 0.989691
6 YXS 0.825758 0.989691
7 0T1 0.809524 0.857143
8 COA 0.809524 0.876289
9 DCA 0.808 0.857143
10 KGA 0.80597 0.819048
11 ETB 0.793651 0.828283
12 FCX 0.792308 0.85
13 FAM 0.792308 0.84
14 30N 0.790698 0.958763
15 CAO 0.790698 0.907216
16 COS 0.790698 0.877551
17 AMX 0.790698 0.865979
18 SCO 0.784615 0.876289
19 CMX 0.784615 0.876289
20 CO6 0.781955 0.896907
21 ACO 0.778626 0.887755
22 MCD 0.774436 0.877551
23 CA6 0.774436 0.93
24 HAX 0.772727 0.84
25 3HC 0.77037 0.886598
26 FYN 0.766917 0.876289
27 3KK 0.766917 0.896907
28 MCA 0.764706 0.907216
29 CAJ 0.762963 0.877551
30 OXK 0.761194 0.896907
31 SOP 0.761194 0.877551
32 COK 0.761194 0.877551
33 A1S 0.757353 0.858586
34 BCO 0.757353 0.877551
35 IVC 0.757353 0.886598
36 CMC 0.755556 0.877551
37 NMX 0.755556 0.8
38 1VU 0.755556 0.887755
39 IRC 0.753623 0.886598
40 YE1 0.751825 0.848485
41 2MC 0.75 0.861386
42 SCD 0.75 0.876289
43 2CP 0.746377 0.887755
44 1HE 0.744526 0.86
45 KGJ 0.744526 0.809524
46 MLC 0.744526 0.896907
47 1GZ 0.741007 0.868687
48 CA8 0.741007 0.93
49 CAA 0.73913 0.886598
50 COO 0.73913 0.877551
51 FAQ 0.735714 0.877551
52 MC4 0.733813 0.852941
53 SCA 0.733813 0.896907
54 3CP 0.728571 0.877551
55 COW 0.728571 0.868687
56 HGG 0.728571 0.896907
57 COF 0.728571 0.841584
58 KFV 0.728571 0.828571
59 BYC 0.728571 0.877551
60 2KQ 0.728571 0.897959
61 BCA 0.723404 0.868687
62 4CA 0.723404 0.85
63 HXC 0.71831 0.878788
64 GRA 0.71831 0.896907
65 1CV 0.717241 0.896907
66 TGC 0.713287 0.887755
67 01A 0.710345 0.825243
68 CIC 0.708333 0.877551
69 CO8 0.708333 0.878788
70 1CZ 0.708333 0.907216
71 S0N 0.708333 0.858586
72 2NE 0.708333 0.86
73 MRR 0.707483 0.878788
74 MRS 0.707483 0.878788
75 0FQ 0.703448 0.858586
76 UCC 0.703448 0.878788
77 DCC 0.703448 0.878788
78 MFK 0.703448 0.878788
79 MYA 0.703448 0.878788
80 4CO 0.703448 0.85
81 ST9 0.703448 0.878788
82 5F9 0.703448 0.878788
83 0ET 0.69863 0.86
84 CS8 0.693878 0.87
85 WCA 0.693878 0.86
86 YNC 0.691275 0.868687
87 DAK 0.691275 0.851485
88 NHM 0.689189 0.86
89 4KX 0.689189 0.851485
90 UOQ 0.689189 0.86
91 NHW 0.689189 0.86
92 HDC 0.689189 0.878788
93 HFQ 0.684564 0.841584
94 J5H 0.68 0.877551
95 8Z2 0.675497 0.87
96 NHQ 0.666667 0.867347
97 F8G 0.660256 0.862745
98 1HA 0.658065 0.86
99 COD 0.656716 0.865979
100 01K 0.653846 0.877551
101 COT 0.649682 0.858586
102 CA3 0.641509 0.858586
103 CCQ 0.64 0.861386
104 7L1 0.633803 0.887755
105 CA5 0.631902 0.825243
106 93P 0.628049 0.868687
107 UCA 0.628049 0.878788
108 CO7 0.610738 0.877551
109 93M 0.609467 0.868687
110 N9V 0.607843 0.85
111 5TW 0.602273 0.84466
112 4BN 0.602273 0.84466
113 COA FLC 0.601399 0.846939
114 OXT 0.6 0.84466
115 JBT 0.568306 0.846154
116 BSJ 0.553073 0.851485
117 HMG 0.54717 0.867347
118 PAP 0.544715 0.71134
119 COA PLM 0.530864 0.85
120 PLM COA 0.530864 0.85
121 PPS 0.519685 0.804124
122 ASP ASP ASP ILE CMC NH2 0.508571 0.84
123 A3P 0.495935 0.701031
124 0WD 0.489933 0.696078
125 SFC 0.473684 0.878788
126 RFC 0.473684 0.878788
127 191 0.463415 0.803738
128 ACE SER ASP ALY THR NH2 COA 0.460733 0.858586
129 PTJ 0.45 0.783505
130 3AM 0.435484 0.690722
131 PAJ 0.431655 0.793814
132 PUA 0.427673 0.722772
133 A22 0.427536 0.714286
134 A2D 0.421875 0.704082
135 HQG 0.42029 0.731959
136 3OD 0.41958 0.742268
137 AGS 0.41791 0.762887
138 SAP 0.41791 0.762887
139 ATR 0.41791 0.701031
140 8LQ 0.417266 0.752577
141 9BG 0.416667 0.696078
142 8LH 0.413043 0.752577
143 ADP 0.412214 0.721649
144 YLB 0.411765 0.816327
145 48N 0.410596 0.747475
146 A2R 0.410072 0.731959
147 8LE 0.408759 0.762887
148 5AL 0.408759 0.731959
149 OAD 0.405594 0.742268
150 NA7 0.405594 0.752577
151 BA3 0.40458 0.704082
152 8QN 0.404255 0.731959
153 HEJ 0.402985 0.721649
154 ATP 0.402985 0.721649
155 SRP 0.402878 0.752577
156 B4P 0.401515 0.704082
157 AP5 0.401515 0.704082
158 YLP 0.401316 0.816327
159 5FA 0.4 0.721649
160 APR 0.4 0.721649
161 AQP 0.4 0.721649
162 AR6 0.4 0.721649
163 2A5 0.4 0.742268
164 FYA 0.4 0.714286
Ligand no: 2; Ligand: LCV; Similar ligands found: 164
No: Ligand ECFP6 Tc MDL keys Tc
1 SO5 1 1
2 LCV 1 1
3 KGP 0.84375 0.989691
4 YZS 0.84375 0.989691
5 YXR 0.825758 0.989691
6 YXS 0.825758 0.989691
7 0T1 0.809524 0.857143
8 COA 0.809524 0.876289
9 DCA 0.808 0.857143
10 KGA 0.80597 0.819048
11 ETB 0.793651 0.828283
12 FCX 0.792308 0.85
13 FAM 0.792308 0.84
14 30N 0.790698 0.958763
15 CAO 0.790698 0.907216
16 COS 0.790698 0.877551
17 AMX 0.790698 0.865979
18 SCO 0.784615 0.876289
19 CMX 0.784615 0.876289
20 CO6 0.781955 0.896907
21 ACO 0.778626 0.887755
22 MCD 0.774436 0.877551
23 CA6 0.774436 0.93
24 HAX 0.772727 0.84
25 3HC 0.77037 0.886598
26 FYN 0.766917 0.876289
27 3KK 0.766917 0.896907
28 MCA 0.764706 0.907216
29 CAJ 0.762963 0.877551
30 OXK 0.761194 0.896907
31 SOP 0.761194 0.877551
32 COK 0.761194 0.877551
33 A1S 0.757353 0.858586
34 BCO 0.757353 0.877551
35 IVC 0.757353 0.886598
36 CMC 0.755556 0.877551
37 NMX 0.755556 0.8
38 1VU 0.755556 0.887755
39 IRC 0.753623 0.886598
40 YE1 0.751825 0.848485
41 2MC 0.75 0.861386
42 SCD 0.75 0.876289
43 2CP 0.746377 0.887755
44 1HE 0.744526 0.86
45 KGJ 0.744526 0.809524
46 MLC 0.744526 0.896907
47 1GZ 0.741007 0.868687
48 CA8 0.741007 0.93
49 CAA 0.73913 0.886598
50 COO 0.73913 0.877551
51 FAQ 0.735714 0.877551
52 MC4 0.733813 0.852941
53 SCA 0.733813 0.896907
54 3CP 0.728571 0.877551
55 COW 0.728571 0.868687
56 HGG 0.728571 0.896907
57 COF 0.728571 0.841584
58 KFV 0.728571 0.828571
59 BYC 0.728571 0.877551
60 2KQ 0.728571 0.897959
61 BCA 0.723404 0.868687
62 4CA 0.723404 0.85
63 HXC 0.71831 0.878788
64 GRA 0.71831 0.896907
65 1CV 0.717241 0.896907
66 TGC 0.713287 0.887755
67 01A 0.710345 0.825243
68 CIC 0.708333 0.877551
69 CO8 0.708333 0.878788
70 1CZ 0.708333 0.907216
71 S0N 0.708333 0.858586
72 2NE 0.708333 0.86
73 MRR 0.707483 0.878788
74 MRS 0.707483 0.878788
75 0FQ 0.703448 0.858586
76 UCC 0.703448 0.878788
77 DCC 0.703448 0.878788
78 MFK 0.703448 0.878788
79 MYA 0.703448 0.878788
80 4CO 0.703448 0.85
81 ST9 0.703448 0.878788
82 5F9 0.703448 0.878788
83 0ET 0.69863 0.86
84 CS8 0.693878 0.87
85 WCA 0.693878 0.86
86 YNC 0.691275 0.868687
87 DAK 0.691275 0.851485
88 NHM 0.689189 0.86
89 4KX 0.689189 0.851485
90 UOQ 0.689189 0.86
91 NHW 0.689189 0.86
92 HDC 0.689189 0.878788
93 HFQ 0.684564 0.841584
94 J5H 0.68 0.877551
95 8Z2 0.675497 0.87
96 NHQ 0.666667 0.867347
97 F8G 0.660256 0.862745
98 1HA 0.658065 0.86
99 COD 0.656716 0.865979
100 01K 0.653846 0.877551
101 COT 0.649682 0.858586
102 CA3 0.641509 0.858586
103 CCQ 0.64 0.861386
104 7L1 0.633803 0.887755
105 CA5 0.631902 0.825243
106 93P 0.628049 0.868687
107 UCA 0.628049 0.878788
108 CO7 0.610738 0.877551
109 93M 0.609467 0.868687
110 N9V 0.607843 0.85
111 5TW 0.602273 0.84466
112 4BN 0.602273 0.84466
113 COA FLC 0.601399 0.846939
114 OXT 0.6 0.84466
115 JBT 0.568306 0.846154
116 BSJ 0.553073 0.851485
117 HMG 0.54717 0.867347
118 PAP 0.544715 0.71134
119 COA PLM 0.530864 0.85
120 PLM COA 0.530864 0.85
121 PPS 0.519685 0.804124
122 ASP ASP ASP ILE CMC NH2 0.508571 0.84
123 A3P 0.495935 0.701031
124 0WD 0.489933 0.696078
125 SFC 0.473684 0.878788
126 RFC 0.473684 0.878788
127 191 0.463415 0.803738
128 ACE SER ASP ALY THR NH2 COA 0.460733 0.858586
129 PTJ 0.45 0.783505
130 3AM 0.435484 0.690722
131 PAJ 0.431655 0.793814
132 PUA 0.427673 0.722772
133 A22 0.427536 0.714286
134 A2D 0.421875 0.704082
135 HQG 0.42029 0.731959
136 3OD 0.41958 0.742268
137 AGS 0.41791 0.762887
138 SAP 0.41791 0.762887
139 ATR 0.41791 0.701031
140 8LQ 0.417266 0.752577
141 9BG 0.416667 0.696078
142 8LH 0.413043 0.752577
143 ADP 0.412214 0.721649
144 YLB 0.411765 0.816327
145 48N 0.410596 0.747475
146 A2R 0.410072 0.731959
147 8LE 0.408759 0.762887
148 5AL 0.408759 0.731959
149 OAD 0.405594 0.742268
150 NA7 0.405594 0.752577
151 BA3 0.40458 0.704082
152 8QN 0.404255 0.731959
153 HEJ 0.402985 0.721649
154 ATP 0.402985 0.721649
155 SRP 0.402878 0.752577
156 B4P 0.401515 0.704082
157 AP5 0.401515 0.704082
158 YLP 0.401316 0.816327
159 5FA 0.4 0.721649
160 APR 0.4 0.721649
161 AQP 0.4 0.721649
162 AR6 0.4 0.721649
163 2A5 0.4 0.742268
164 FYA 0.4 0.714286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6n96.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6n96.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6n96.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6n96.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 6n96.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 6n96.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 6n96.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 6n96.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 6n96.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 6n96.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 6n96.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 6N96; Ligand: SO5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 6n96.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 6n96.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 6N96; Ligand: LCV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 6n96.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback